htsjdk.tribble.gff

Class Gff3Writer

java.lang.Object

htsjdk.tribble.gff.Gff3Writer

All Implemented Interfaces:

java.io.Closeable, java.lang.AutoCloseable

public class Gff3Writer
extends java.lang.Object
implements java.io.Closeable

A class to write out gff3 files. Features are added using addFeature(Gff3Feature), directives using addDirective(Gff3Codec.Gff3Directive), and comments using addComment(String). Note that the version 3 directive is automatically added at creation, so should not be added separately.

Constructor Summary

Constructors

Constructor and Description
Gff3Writer(java.io.OutputStream stream)
Gff3Writer(java.nio.file.Path path)

Method Summary

Modifier and Type	Method and Description
void	addComment(java.lang.String comment) Add comment line
void	addDirective(Gff3Codec.Gff3Directive directive) Add a directive
void	addDirective(Gff3Codec.Gff3Directive directive, java.lang.Object object) Add a directive with an object
void	addFeature(Gff3Feature feature) add a feature
void	close()
protected java.lang.String	escapeString(java.lang.String s) escape a String.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

Gff3Writer

public Gff3Writer(java.nio.file.Path path)
           throws java.io.IOException

Throws:

java.io.IOException

Gff3Writer

public Gff3Writer(java.io.OutputStream stream)

Method Detail

addFeature

public void addFeature(Gff3Feature feature)
                throws java.io.IOException

add a feature

Parameters:

feature - the feature to be added

Throws:

java.io.IOException

escapeString

protected java.lang.String escapeString(java.lang.String s)

escape a String. Default behavior is to call encodeString(String)

Parameters:

s - the string to be escaped

Returns:

the escaped string

addDirective

public void addDirective(Gff3Codec.Gff3Directive directive,
                         java.lang.Object object)
                  throws java.io.IOException

Add a directive with an object

Parameters:

directive - the directive to be added

object - the object to be encoded with the directive

Throws:

java.io.IOException

addDirective

public void addDirective(Gff3Codec.Gff3Directive directive)
                  throws java.io.IOException

Add a directive

Parameters:

directive - the directive to be added

Throws:

java.io.IOException

addComment

public void addComment(java.lang.String comment)
                throws java.io.IOException

Add comment line

Parameters:

comment - the comment line (not including leading #)

Throws:

java.io.IOException

close

public void close()
           throws java.io.IOException

Specified by:

close in interface java.io.Closeable

Specified by:

close in interface java.lang.AutoCloseable

Throws:

java.io.IOException